Jan. 27th 2015

  • Goal : To identify DNA methylation markers which the difference in methylation are associated with change in PHQ (~ Aim 2)

  • Model : PHQchange = a + b * Methylation Difference + e

  • Sites : 483522

  • Sample size: 37

  • Multiple Testing Correction : Bonferroni

  • 5% MinP Cutoff - raw PHQchange: 5.34e-09

  • 5% MinP Cutoff - INV PHQchange: 1.40e-07

Association Test

PHQchange ~ Difference in Methylation

QQplot of pvals based on Raw PHQchange and CI

Results based on Raw PHQchange
CpG Chr Pos Genes pval p.adj size
cg00886598 5 42812844 SEPP1 2.0e-07 0.0847 37
cg20292653 2 5847374 NA 2.0e-07 0.1146 37
cg05518543 4 1283165 MAEA 3.0e-07 0.1417 37
cg20049415 20 21377671 NKX2-4 8.0e-07 0.3735 37
cg07432626 5 146889536 NA 1.0e-06 0.4969 37
cg10059942 10 124908488 HMX2 3.6e-06 1.0000 37
cg10169763 16 87873389 SLC7A5 4.4e-06 1.0000 37
cg03625512 12 125569850 AACS 4.4e-06 1.0000 37
cg24601967 1 6366496 ACOT7 5.4e-06 1.0000 37
cg07678449 4 171011395 AADAT 6.5e-06 1.0000 37

Residual QQ plots top 6 sites - raw PHQchange

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Leverage Plots top 6 sites - raw PHQchange

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Cook's Distance - raw PHQchange

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PCA on top sites - Scree Plot

PCA on top sites - biplot

Association Test

INV PHQchange ~ Difference in Methylation

QQplot of pvals based on INV PHQchange

QQplot : Nonfiltered vs filtered

Results based on INV PHQchange
CpG Chr Pos Genes pval p.adj size
cg20292653 2 5847374 NA 4.00e-07 0.1932 37
cg05706582 7 2566911 LFNG 5.50e-06 1.0000 37
cg09640960 20 60794676 HRH3 7.00e-06 1.0000 37
cg23026478 6 46706037 NA 1.03e-05 1.0000 37
cg00886598 5 42812844 SEPP1 1.28e-05 1.0000 37
cg10169763 16 87873389 SLC7A5 1.55e-05 1.0000 37
cg09405169 3 12329745 PPARG 3.26e-05 1.0000 37
cg14912788 1 3661862 KIAA0495 3.41e-05 1.0000 37
cg13883397 11 61900852 INCENP 3.49e-05 1.0000 37
cg12405983 19 58630240 ZSCAN18 3.69e-05 1.0000 37

Residual QQ plots top 6 sites - INV PHQchange

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## 63127 
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Leverage Plots top 6 sites - INV PHQchange

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Cook's Distance - INV PHQchange

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PCA on top sites - Scree Plot

PCA on top sites - biplot

Association Test

INV PHQchange ~ INV Difference in Methylation

QQplot pvals : INV PHQchange ~ INV Diff Methyl

ScatterPlot: -log10 InvDiffMethyl vs -log10 DiffMethyl

Results based on INV PHQchange ~ INV Base Methylation
CpG Chr Pos Genes pval p.adj size
21 cg20292653 2 5847374 NA 2.00e-07 0.0841 37
5 cg05706582 7 2566911 LFNG 3.00e-06 1.0000 37
16 cg14458654 3 174095293 NA 6.20e-06 1.0000 37
15 cg10917153 15 42448786 PLA2G4F 8.80e-06 1.0000 37
25 cg23093450 17 40172452 NKIRAS2 1.57e-05 1.0000 37
13 cg10169763 16 87873389 SLC7A5 1.85e-05 1.0000 37
17 cg14912788 1 3661862 KIAA0495 1.89e-05 1.0000 37
10 cg09800975 10 6130861 RBM17 2.02e-05 1.0000 37
23 cg22523072 1 248300255 NA 2.06e-05 1.0000 37
4 cg05518543 4 1283165 MAEA 2.22e-05 1.0000 37

Residual QQ plots top 6 sites

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Leverage Plots top 6 sites

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Cook's Distance

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PCA on top sites - Scree Plot

PCA on top sites - biplot